Barrels, magnets, and flying insects

Bunch of new reviews by Brandeis authors in press, check one out if you need to catch up on the state of the art.

  • Lisman J, Yasuda R, Raghavachari S. Mechanisms of CaMKII action in long-term potentiation. Nat Rev Neurosci. 2012.
  • Griffith LC. Identifying behavioral circuits in Drosophila melanogaster: moving targets in a flying insect. Curr Opin Neurobiol. 2012.
  • Hedstrom L. The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (beta/alpha)(8) barrel enzymes. Crit Rev Biochem Mol Biol. 2012.
  • Pan Y, Du X, Zhao F, Xu B. Magnetic nanoparticles for the manipulation of proteins and cells. Chem Soc Rev. 2012.

A Little Freedom Makes a Big Difference

As enzymes evolve over time, proteins of similar structure acquire small sequence changes and acquire new activities. What are the key changes in an enzyme’s structure or mechanism that allow this to happen? Researchers from the Hedstrom lab, led by former postdoc Gregory Patton, in collaboration with researchers from the Karolinska Institute, investigated this question in the case of two proteins, inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR). The enzymes share similar structural features but carry out different reactions in a cell. Since the two enzymes are in opposing pathways, there could be severe consequences if the enzymes slip and carry out the ‘other’ reaction.

The results, published last month in Nature Cell Biology, argue strongly that the difference is based on the ability of the enzyme to switch between two conformations. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR, including states in which the cofactor (NAD or NADP) is either in an ‘in’ conformation poised for hydride transfer (below, right), or an ‘out’ conformation in which the cofactor is 6 Å from IMP (below, left).

Using mutagenesis along with kinetic experiments, the group demonstrates that the ‘out’ conformation is required for the deamination of GMP. The accessibility of this conformation at the key step in GMPR but not IMPDH seems to determine the two different outcomes — thus, the freedom of the enzyme and cofactor to carry out a conformational change determines the specificity.

An interesting question, looking at the pathways, is whether GMPR can ‘run in reverse’, catalyzing the direct amination of IMP to form GMP (and saving the cell some energy in the process).  Overexpression of GMPR does allow E. coli to survive in the absence of IMPDH and GMPS, demonstrating that GMPR-driven synthesis of GMP can support life.  Indeed, some modern organisms that live in ammonia-rich environments appear to obtain GMP by this strategy.  If life began in an ammonia rich environment as is often proposed, the ancestral purine biosynthetic pathways may have produced GMP via GMPR.

For more details, see the paper:  Patton GC, Stenmark P, Gollapalli DR, Sevastik R, Kursula P, Flodin S, Schuler H, Swales CT, Eklund H, Himo F, Nordlund P, Hedstrom L. Cofactor mobility determines reaction outcome in the IMPDH and GMPR (beta-alpha)(8) barrel enzymes. Nat Chem Biol. 2011.

Novel IMPDH inhibitors are candidates for antibacterial drugs

The rise of multiply drug resistant bacteria creates an urgent need for new antibiotics and novel antibiotic targets.  IMPDH, a key enzyme in the biosynthesis of RNA/DNA precursors, is a target for cancer therapy that has not been exploited in antibiotic development. In their recent paper in Chemistry & Biology entitled Structural determinants of inhibitor selectivity in prokaryotic IMP dehydrogenases, Prof. Lizbeth Hedstrom and Brandeis postdocs Deviprasad Golapalli, Iain MacPherson and Suresh Gorla show that selective inhibitors of IMPDH from the protozoan parasite Cryptosporidium parvum also exhibit antibacterial activity. This work could lead to novel treatments for a wide variety of bacterial infections, including some of the most devastating and troubling human pathogens: Mycobacterium tuberculosis, drug-resistant Staphylococcus aureus (e.g. MRSA and VRSA), drug resistant Streptococcus pneumoniae and select agents such as Bacillus anthracis, Burkholderia mallei/pseudomallei and Francisella tularensis.  Importantly, these compounds will spare some commensal bacteria, which should decrease side effects and slow the rise of resistance.  This work suggests that IMPDH-targeted inhibitors can be developed into a new class of broader spectrum antibiotics.

New structural model for IMPDH

Members of the Hedstrom lab have cooked up a new structural model for inosine-5′-monophosphate dehydrogenase (IMPDH), see below:

Confectioner's model of IMPDH

Edible model of IMPDH

IMPDH and retinal degeneration

Recent work from the Hedstrom Lab suggests an explanation for how mutations in this enzyme involved in nucleotide biosynthesis can lead to retinal degeneration and hereditary blindness. It seems it has to do with binding mRNA. Read more at:

Protected by Akismet
Blog with WordPress

Welcome Guest | Login (Brandeis Members Only)